The seat stays were a problem, and Rans has changed that. I have that type on my 2007 Stratus LE.
I broke off the plastic piece above the idleers when my chain dropped off my big cog and ripped the wheel out of the drops. I replaced it using stainless steel screws and nuts with plastic ice machine tubing covering the screw. Your solution with a pen body sounds good.
Don't know about your seat mesh, but I don't keep anything in my pockets if I can avoid it, so it doesn't concentrate pressure at one point.